Katherine Eaton

That makes perfect sense thank you! Giving these clades names is super helpful, otherwise they previously got misassigned to `XM` just as you indicate. @AngieHinrichs can I ask how you...

Wow, you preemptively answered all of my follow-up questions! > At this point, the misc/proposed labels are replaced with BA.2 or BA.1 depending on which parent lineage donated more mutations...

> If you're open to trying Micromamba: it doesn't have those kinds of problems. I couldn't get any of the suggested fixes in these threads to work, so I switched...

This is a great suggestion thank you! I can make this a command-line parameter (`--entrez-max-tries 3`) and a configuration option the same way `FORCE_PAUSE_SECONDS` is setup.

Thanks for the suggestion! I unfortunately know very little about developing with PostgeSQL and MySQL. But maybe this is just the push I need to learn! The complexity I'm most...

> Perhaps using SQLAlchemy would be a good idea to interface with the database. I've just started working with SQLAlchemy and PostgreSQL for a separate project. Once I've gained a...

That actually clarifies things a lot, thanks! Is my understanding of the current workflow correct: - `data/sequences.fasta` should contain all possible sequences. - Which might include sequences from lapis, gisaid,...

Hi Marie, Here's my understanding of the problematic parameters. - `--clades all`: consider all clades defined in `mapping.csv` as potential parents. As of bd2a4009, there are `36` potential clades. -...

Sorry, the code for both of these is: ```bash python3 sc2rf.py pango_designation_590.fasta --ansi --unique 1 --enable-deletions ```

Hi @BenjaminDelisle, I think for XT, the flag `--unique 1` is required, because there is only 1 SNP contributed by a BA.1 parent (A26530G). For added confidence, the flag `--enable-deletions`...